MolNFT v1 · #100789 · protein
X-ray crystal structure of streptococcus sanguinis DIMANGANESE(II)- nrdf
4N83 · Ribonucleoside-diphosphate reductase subunit beta: “X-ray crystal structure of streptococcus sanguinis DIMANGANESE(II)- nrdf”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.77). MolNFT v1 #100789 on GenesisL1: 3D…
- PDB
- 4N83
- Type
- protein
- Length
- 2,271 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit beta
- EC
- 1.17.4.1
- UniProt
- A3CLZ4
- Ligands
- MN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 285 | 75% helix, 0% strand | A3CLZ4 |
| B, C, D, E, F | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 284 | 78% helix, 0% strand | A3CLZ4 |
| G, H | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 283 | 78% helix, 0% strand | A3CLZ4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.77 | 0.80 | 72 | empty |
| 2 | 931 | 0.76 | 0.79 | 67 | empty |
| 3 | 787 | 0.74 | 0.79 | 57 | empty |
| 4 | 121 | 0.54 | 0.82 | 14 | empty |
| 5 | 278 | 0.52 | 0.75 | 27 | empty |
Interfaces
14 interfaces between chains.
- E–F · 2229 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2226 Ų buried · 34 hydrogen bonds · protein-protein
- B–H · 2205 Ų buried · 37 hydrogen bonds · protein-protein
- A–G · 2204 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 438 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4N83 · X-ray crystal structure of Streptococcus sanguinis dimanganese(II)-NrdF · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A3CLZ4
- Elsewhere: RCSB PDB 4N83 · PDBe 4N83 · UniProt A3CLZ4
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